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Major and trace elements of sediments from two gravity cores (10YDY09 and 12I712) in the northeastern Indian Ocean have been analyzed for sediment provenance and the relationship of the sediments with climate change since 50 ka. The rare earth element (REE) compositions were analyzed, and the sediment contributions were estimated for the major potential sources, including the Ganges-Brahmaputra (G-B), Godavari-Krishna (G-K) and Mahanadi Rivers. Our results showed that the sediments in the study area were a mixture of sediments discharged from the above three rivers. The sediment contribution of the G-K Rivers increased notably during the Holocene when the rainfall increased, which may be caused by the strengthening of the East Indian Coastal Current (EICC) and the resulting large amounts of sediments supplied by the G-K Rivers. The higher sediment contribution from the G-B Rivers demonstrated the role of the Active Channel in transporting sediments to the distal Bengal Fan. During the last glacial maximum (LGM), especially in the late period, the Indian summer monsoon weakened, but the winter monsoon strengthened, resulting in a decrease in chemical weathering and elemental enrichment in the northeastern Indian Ocean. Conversely, when the rainfall was low, the chemical weathering strengthened and K2O/TiO2 ratios were lowered due to the longer weathering time and resulting sediment potassium loss. However, when the sea level reached a certain height during the Holocene, the fluvial sediments could not easily enter deep-water environments through submarine channels, which were well developed in the Bengal Fan.